The owners of a ship at the centre of a major oil spill off south-east Queensland two years ago have indicated they will plead guilty over the environmental disaster.

The Swire Navigation and Bluewind Shipping Limited-owned ship the MV Pacific Adventurer lost 31 containers in heavy seas off Cape Moreton in March 2009.

Some of the containers hit the vessel, causing a 270,000-litre fuel oil spill along Moreton and Bribie islands and Sunshine Coast beaches - Queensland's largest natural disaster.

Maritime Safety Queensland general manager Patrick Quirk says the owners have advised the Brisbane District Court they intend to plead guilty as charged under the Transport Operations Marine Pollutions Act.

"It's been a pleasing outcome this afternoon, although it is not the final part," he said.

"We need to go through the final part of the court process and we need to respect that, but it has been a long investigation, a long process since those dark days in March 2009, and we are happy it is coming to a conclusion."

Charges have been dropped against the ship's master, Bernardino Santos, because he had only recently taken over the ship and the problem causing the containers to come loose existed before his arrival.

The guilty plea will be entered and sentencing submissions will be heard by the court on October 12.